Hello @zack100
Shopify dawn latest version have some other features of customized theme. as you said you have done JS , CSS code customization then when you update the theme it may have some changes or modification on your current theme if you will do manual update then it may take time to update manually for your theme you will have to customized from the scratch. In your case I recommend performing a manual update and then re-configuring apps you plan to keep, and re-adding any custom. Theme upgrade is time consuming work you need to have liquid and coding knowledge.
Any customization made to your theme using the Theme Editor are copied over and applied to the updated theme. These include:
Changing theme settings
Changing page layouts, like adding, reordering, removing, or hiding sections or blocks
Changing section or blocks’ settings, including adding images, videos, text, and data sources
Adding new templates
Adding, removing, or changing settings of app embeds or app extensions
Manual code changes to your theme files through the Code Editor (except files in the /templates folder and settings_data.json).